RNA-SEQ: Low % of Alignment
I have performed Alignment of my RNA-seq paired-end FASTQ files to Reference human hg19 genome using HISAT2. However, I got a low % alignment (34.6%) for one of my samples. What are the possible consequence if I generate a count file from such a BAM file. Is it possible I miss out on few genes or get low expression ??
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Yes, the last sentence may apply here. I would see why the alignment is bad, try to blast a couple of the unmapped reads to get an idea.
Thank you for your reply. Since I am new to RNA-Seq, I do not have an idea of getting unmapped reads. How can I obtain those unmapped reads?
How do I find unmapped reads in my sam file?
How To Get Unmapped Reads From A Bam File Obtained Using Gsnap And Convert It Into A Fastq File?